Web interfaces¶

Biobrick¶

GET /biobrick/<type>

Get a list of all available biobricks of some type. <type> can be one of input, output, receptor, promoter, RBS.

Example:

{
  "result": [
    {"type": "input", "name": "Input XXX", "id": 1234},
    {"type": "input", "name": "Input YYY", "id": 5687},
    ...]
}

GET /biobrick/<type>?id=XXX

Get the information of a biobrick specified by <type> and ID.

Example:
```
{
  "result": {"type": "input", "name": "Input XXX", "id": 1234}
}
```

GET /biobrick/suggest/promoters?input_id=XXX

Get the suggested promoters according to the chosen input.

Example:

{
  "result": [
    {"type": "promoter", "name": "Promoter XXX", "id": 1234},
    {"type": "promoter", "name": "Promoter YYY", "id": 5687},
    ...]
}

GET /biobrick/suggest/receptors?input_id=XXX&promoter_id=YYY

Get the suggested receptors according to the chosen input and promoter.

Example:

{
  "result": [
    {"type": "receptor", "name": "Receptor XXX", "id": 1234},
    {"type": "receptor", "name": "Receptor YYY", "id": 5687},
    ...]
}

Circuit Design¶

POST /circuit/schemes

Design a circuit according to a given truth table. Only the design frames that can be interpreted as boolean logic gates would be used.

Example of request:

{
  "inputs": [
    { "receptor_id": 1, "id": 1, "promoter_id": 17 },
    { "receptor_id": 3, "id": 2, "promoter_id": 23 }
  ],
  "truth_table": [
    { "inputs": [ true, true ], "outputs": [ true, true ] },
    { "inputs": [ false, true ], "outputs": [ false, true ] },
    { "inputs": [ true, false ], "outputs": [ false, true ] },
    { "inputs": [ false, false ], "outputs": [ false, false ] }
  ],
  "outputs": [ 2, 4 ]
}

Notice: The truth table provided can be uncompleted. In such cases, schemes that satisfy all rows of the truth table will be return.

Example of response:

{
  "inputs": [
    [{/* input */}, {/* receptor */}],
    [{/* input */}, {/* receptor */}]
  ],
  "logics": [
    [{/* candidate for output 1 */}, {/* candidate for output 1 */}],
    [{/* candidate for output 2 */}, {/* candidate for output 2 */}]
  ]
}

POST /circuit/details

Get the detailed information of a user-designed circuit.

Example of request:

{
  "inputs": [
    { "receptor_id": 12, "id": 8, "promoter_id": 1 },
    { "receptor_id": 13, "id": 9, "promoter_id": 17 }
  ],
  "logics": [ 23, 21 ],
  "outputs": [ 1, 2 ]
}

Example of response:

{
  "inputs": [
    [{/* input */}, {/* receptor */}],
    [{/* input */}, {/* receptor */}]
  ],
  "logics": [
    {/* logic for output 1 */},
    {/* logic for output 2 */}
  ],
  "dna": [
    [ "BBa_K346002", "promoter", "TTCCATATCGCTTGACTCCGTACATGAGTACGGA..." ],
    [ "", "biobrick_scar", "TACTAGAG" ],
    [ "BBa_B0034", "RBS", "AAAGAGGAGAAA" ],
    /* ... */
  ],
  "dna_export": "TTCCATATCGCTTGACTCCGTACATGAGTACGGAAGTAAGG........"
}

Simulation¶

POST /simulation/preprocess

Preprocess the circuit design for simulation. Preprocessing is required before simulation because the regulary relationships and some other necessary information need to be retrieved from the design.

The request is the same as that of POST /circuit/details.

Example of response:
```
{
  "inputs": [ "Mercury ions" ],
  "output_RBS": { "BBa_E1010": "BBa_B0034" },
  "outputs": [ "BBa_E1010" ],
  "reactants": [ "BBa_E1010", "Mercury ions" ],
  "relationships": [
    {
      "K": 0.0021,
      "from": "Mercury ions",
      "gamma": 0.122,
      "n": 1.2,
      "to": "BBa_E1010",
      "type": "BIREPRESS"
    }
  ]
}
```
The output_RBS of the preprocessing result can be change before simulation. The changes of RBS will result in the changes of the values of alpha in the simulation.

POST /simulation/simulate/static

Static simulation. The concentration of one of the input will be constant and the concentration of the other input will vary.

Example of request:

{
  "output_RBS": {/* ... */},
  "reactants": [/* ... */],
  "relationships": [/* ... */],
  "c_static": 1.0, /* The concentration of the static input */
  "t": 200  /* Time of reaction */
}

Example of response:

{
  "c_input": [
    0.0001, 0.000316227766017, 0.001, 0.00316227766017,
    0.01, 0.0316227766017, 0.1, 0.316227766017, 1.0
  ],
  "c_output": [
    {
      "variable": "Mercury ions",
      "c": {
        "BBa_E1010": [
          0.30411990073366146,
          1.1259746535556292,
          3.5056683139687936,
          7.472784059484611,
          10.440528797897906,
          11.59745840267149,
          11.929511156553845,
          12.015928637653683,
          12.037832830968352
        ]
      }
    }
  ]
}

POST /simulation/simulate/dynamic

Dynamic simulation. Give a initial concentrations of all reactant and observe how the concentrations change over time.

Example of request:

{
  "output_RBS": {/* ... */},
  "reactants": [/* ... */],
  "relationships": [/* ... */],
  "x0": {  /* Initial concentrations */
    "Arsenic ions": 0.003, "aTc": 0.001, "Zinc ions": 0.01, "PAI": 0.004
  },
  "t": 200  /* Time of reaction */
}

Example of response:

{
  "t": [
    0.0, 5.0, 10.0, 15.0, 20.0, 25.0, 30.0, 35.0, 40.0, 45.0,
    50.0, 55.0, 60.0, 65.0, 70.0, 75.0, 80.0, 85.0, 90.0, 95.0, 100.0
  ],
  "c": {
    "BBa_E1010": [
      0.0, 3.5471085416412245, 5.889406992324342, 7.436121010414228,
      8.457478469975687, 9.13192179697643, 9.577283724437871, 9.871374589156435,
      10.065573879777089, 10.193812488166891, 10.278493174372407,
      10.334411396488303, 10.371336552680521, 10.395719787844786,
      10.411821064545714, 10.422453415407007, 10.429474404297356,
      10.434110658841762, 10.437172172901423, 10.439193819523224,
      10.440528797897906
    ]
  }
}

FLAME documentation

Web interfaces

Web interfaces¶

Biobrick¶

Circuit Design¶

Simulation¶